Introduction
Before collecting a single sample, it’s important to think through
the full design of your eDNA project. This section introduces the
considerations and protocols for preparing and collecting high-quality
eDNA samples in both field and museum environments.
Designing an eDNA Study
What’s the research question?
- Are you detecting a specific species or surveying communities?
- Temporal and spatial scales matter.
Choosing the right marker
- Based on your taxa of interest (e.g., COI for animals, 18S for
eukaryotes).
- Consider ecosystem and sample type (water vs. sediment
vs. swabs).
Consider DNA persistence
- Environmental DNA degrades over time.
- Degradation influenced by UV light, temperature, pH, microbial
activity.
Sampling Environments
Aquatic Sampling
- Surface water, mid-column, sediment cores.
- Marine and freshwater protocols differ in filtration volume and
salinity handling.

Terrestrial and Air Sampling
- Soil or snow sampling using sterile scoops or syringes.
- Air filters or cyclone samplers for airborne DNA.
Museum Settings
- Swabbing collection surfaces, containers, or tools.
- Extracting DNA from ethanol or residual fluids.
Filtration and Preservation
Filter Types
- Sterivex (enclosed, on-site filtration)
- Glass fiber or cellulose nitrate filters (lab filtration)
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